Finding attractors in asynchronous Boolean dynamics

DOI10.1142/S0219525911003098MaRDI QIDQ3018440zbMATH OpenOpenAlexFDO

Authors Thomas Skodawessely, Konstantin Klemm

Publication date 27 July 2011

Published in Advances in Complex Systems (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1008.3851

zbMATH Keywords

algorithmattractorsBoolean network

Mathematics Subject Classification ID

Applications of graph theory (05C90) Dynamical systems in biology (37N25) Computational methods for problems pertaining to biology (92-08) Systems biology, networks (92C42)

Abstract: We present a computational method for finding attractors (ergodic sets of states) of Boolean networks under asynchronous update. The approach is based on a systematic removal of state transitions to render the state transition graph acyclic. In this reduced state transition graph, all attractors are fixed points that can be enumerated with little effort in most instances. This attractor set is then extended to the attractor set of the original dynamics. Our numerical tests on standard Kauffman networks indicate that the method is efficient in the sense that the total number of state vectors visited grows moderately with the number of states contained in attractors.

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Cites work

• ASYNCHRONOUS AUTOMATA NETWORKS CAN EMULATE ANY SYNCHRONOUS AUTOMATA NETWORK
• Improving the efficiency of attractor cycle identification in Boolean networks
• SIMPLIFYING BOOLEAN NETWORKS
• Superpolynomial growth in the number of attractors in Kauffman networks

Cited in

(16)

• Uncovering operational interactions in genetic networks using asynchronous Boolean dynamics
• P\(_-\)UNSAT approach of attractor calculation for Boolean gene regulatory networks
• Compositional analysis of Boolean networks using local fixed-point iterations
• Attractor analysis of asynchronous Boolean models of signal transduction networks
• Controllability of Boolean control networks under asynchronous stochastic update with time delay
• Vanishing configurations in network dynamics with asynchronous updates
• Controllability of Boolean networks via input controls under Harvey's update scheme
• Attractor computation using interconnected Boolean networks: testing growth rate models in \textit{E. coli}
• An ASP-based approach for attractor enumeration in synchronous and asynchronous Boolean networks
• Attractors and transient in sequential dynamical systems
• Detecting attractors in biological models with uncertain parameters
• Boolean dynamics revisited through feedback interconnections
• SAF: SAT-based attractor finder in asynchronous automata networks
• Attractor identification in asynchronous Boolean dynamics with network reduction
• The attractor structure of functional connectivity in coupled logistic maps
• An integer programming framework for identifying stable components in asynchronous Boolean networks

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